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| Open AccessTheory and simulations of condensin mediated loop extrusion in DNA
How chromosomes, which are polymers with nearly billion base pairs, are packaged in the restricted nuclear volume is not well understood. Here, the authors combine polymer physics, nonequilibrium fluctuation theorem, and simulations to quantitatively predict the force-dependent velocity and step-size distribution of condensin, which facilitates the folding of chromosomes by loop extrusion.
- Ryota Takaki
- , Atreya Dey
- & D. Thirumalai
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Article
| Open AccessEfficient generative modeling of protein sequences using simple autoregressive models
Deep learning is a powerful tool for the design of novel protein sequences, yet can be computationally very inefficient. Here the authors propose using simple forecasting models to efficiently generate a large number of novel protein structures.
- Jeanne Trinquier
- , Guido Uguzzoni
- & Martin Weigt
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Article
| Open AccessEmergence and melting of active vortex crystals
Whereas transitions from solid- to fluid-like states in systems of active particles have received much attention, the characterization of phase transitions in active fluids with self-organized vortices so far has remained elusive. James et al. take us on a numerical tour de force from active turbulence to active vortex crystals.
- Martin James
- , Dominik Anton Suchla
- & Michael Wilczek
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Article
| Open AccessCell migration guided by long-lived spatial memory
Cells can modify their environment by depositing biochemical signals or mechanically remodelling the extracellular matrix; the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here authors show that motile cells leave long-lived physicochemical footprints along their way, which determine their future path.
- Joseph d’Alessandro
- , Alex Barbier--Chebbah
- & Benoît Ladoux
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Article
| Open AccessProton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells
Controlled actuation is an important aspect of synthetic cellular systems. Here, the authors combine pH responsive DNA origami structures with light triggered proton pump engineered E. coli to trigger a change in pH and control the deformation of giant unilamellar vesicles by simple illumination.
- Kevin Jahnke
- , Noah Ritzmann
- & Kerstin Göpfrich
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Article
| Open AccessVimentin intermediate filaments stabilize dynamic microtubules by direct interactions
The tasks of the cytoskeleton depend on the fine-tuned interplay between the three filamentous components: actin filaments, microtubules, and intermediate filaments. Here, the authors show in a reconstituted in vitro system that vimentin intermediate filaments stabilize microtubules against depolymerization and support microtubule rescue by direct interactions.
- Laura Schaedel
- , Charlotta Lorenz
- & Sarah Köster
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Article
| Open AccessCurvature in the reproductive tract alters sperm–surface interactions
The effect of fallopian tube’s curvature on sperm motion has not been studied in detail. Here, the authors use droplet microfluidics to create soft curved interfaces, revealing a dynamic switch in sperm motility from a progressive surface-aligned mode at low curvatures, to an aggressive surface-attacking mode at high curvatures.
- Mohammad Reza Raveshi
- , Melati S. Abdul Halim
- & Reza Nosrati
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Article
| Open AccessBulk-surface coupling identifies the mechanistic connection between Min-protein patterns in vivo and in vitro
Self-organisation of Min protein patterns observed in vivo and in vitro differ qualitatively and quantitatively. Here the authors reconstituted Min proteins in laterally wide microchambers with a well-controlled height and show that the Min protein dynamics on the membrane crucially depend on the micro chamber height.
- Fridtjof Brauns
- , Grzegorz Pawlik
- & Cees Dekker
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Article
| Open AccessCooperative stator assembly of bacterial flagellar motor mediated by rotation
Ito and co-workers unravel how bacteria such as Salmonella switch gears with their flagellar driving machinery. External load triggers the dynamic remodeling of the molecular complex sustaining the torque, and the number of stator units is adapted in a non-trivial, cooperative manner.
- Kenta I. Ito
- , Shuichi Nakamura
- & Shoichi Toyabe
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Article
| Open AccessExcitonic structure and charge separation in the heliobacterial reaction center probed by multispectral multidimensional spectroscopy
The primary energy conversion step in photosynthesis, charge separation, takes place in the reaction center. Here the authors investigate the heliobacterial reaction center using multispectral two-dimensional electronic spectroscopy, identifying the primary electron acceptor and revealing the charge separation mechanism.
- Yin Song
- , Riley Sechrist
- & Jennifer P. Ogilvie
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Article
| Open AccessMechanical plasticity of collagen directs branch elongation in human mammary gland organoids
Mammary organoid growth from single primary human cells rely on distinct morphogenetic processes. Here, the authors observe by live cell imaging the importance of the plastic mechanical response of the extracellular matrix and cell migration for the underlying arborized structure formation process.
- B. Buchmann
- , L. K. Engelbrecht
- & A. R. Bausch
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Article
| Open AccessFtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division
Bacterial cell division by cell wall synthesis proteins is guided by treadmilling filaments of the cytoskeleton protein FtsZ. Here authors use nanofabrication, advanced microscopy, and microfluidics to resolve the function of FtsZ treadmilling in the Gram-positive model organism Bacillus subtilis.
- Kevin D. Whitley
- , Calum Jukes
- & Séamus Holden
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Article
| Open AccessStatistics of pathogenic bacteria in the search of host cells
Chemotaxis may generally be thought to determine bacterial virulence and identification of appropriate host cells. Here, Otte, Ipiña et al. show that if this process is studied in vitro, purely mechanistic random search strategies must be included to explain the experimental results.
- Stefan Otte
- , Emiliano Perez Ipiña
- & Fernando Peruani
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Article
| Open AccessLearning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales
The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, the authors develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus.
- Joris J. B. Messelink
- , Muriel C. F. van Teeseling
- & Chase P. Broedersz
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Article
| Open AccessActive carpets drive non-equilibrium diffusion and enhanced molecular fluxes
Fick’s laws describe the essential physics of diffusion, but it is challenging to extend them to systems out of equilibrium. The authors derive the diffusivity of particles near active carpets - a surface covered with hydrodynamic actuators, which provides a framework for transport in living matter.
- Francisca Guzmán-Lastra
- , Hartmut Löwen
- & Arnold J. T. M. Mathijssen
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Article
| Open AccessHinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity
TEM-1 β-lactamase evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency and degrades β-lactam antibiotics with a strong preference for penicillins. Here authors developed a computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism and show a putative Precambrian β-lactamase that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements.
- Tushar Modi
- , Valeria A. Risso
- & S. Banu Ozkan
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Article
| Open AccessMarkerless tracking of an entire honey bee colony
Honey bee colonies are hard to automatically monitor due to the high number of visually similar members which move rapidly and whose numbers change over time. Here, the authors report a method for markerless tracking of a bee colony by adapting convolutional neural networks for detection and tracking.
- Katarzyna Bozek
- , Laetitia Hebert
- & Greg J. Stephens
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Article
| Open AccessQuantifying information accumulation encoded in the dynamics of biochemical signaling
Understanding how cells discriminate between stimuli is an ongoing challenge. Here, the authors propose a mathematical framework for inferring the mutual information encoded in temporal signaling dynamics and use it to study how information is transmitted over time in response to different stimuli in NFκB, MAPK and p53 signaling pathways.
- Ying Tang
- , Adewunmi Adelaja
- & Alexander Hoffmann
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Article
| Open AccessSniffing speeds up chemical detection by controlling air-flows near sensors
Sniff frequency naturally varies with animal type due to allometric scaling. Using data from live animals and a machine olfactory system, Spencer et al. reveal a deeper reason for sniffing with implications for designing gas detectors: the sniff is adapted to efficient odor detection.
- Thomas L. Spencer
- , Adams Clark
- & David L. Hu
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| Open AccessHarnessing peak transmission around symptom onset for non-pharmaceutical intervention and containment of the COVID-19 pandemic
Transmission by pre-symptomatic and asymptomatic viral carriers makes intervention and containment of the COVID-19 extremely challenging. Here, the authors construct an epidemiological model that focuses on transmission around the symptom onset, exploring specific transmission control measures.
- Liang Tian
- , Xuefei Li
- & Lei-Han Tang
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Article
| Open AccessReentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions
Elucidating the molecular driving forces underlying liquid–liquid phase separation is a key objective for understanding biological function and malfunction. Here the authors show that a wide range of cellular proteins, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, which form condensates at low salt concentrations, can reenter a phase-separated regime at high salt concentrations.
- Georg Krainer
- , Timothy J. Welsh
- & Tuomas P. J. Knowles
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Article
| Open AccessIrreversibility in dynamical phases and transitions
The degree of irreversibility of a dynamical system is commonly characterized by the total rate of entropy production. Seara et al. introduce a measure that quantifies irreversibility from data in broad classes of spatiotemporal non-equilibrium systems.
- Daniel S. Seara
- , Benjamin B. Machta
- & Michael P. Murrell
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Article
| Open AccessFrom deterministic to fuzzy decision-making in artificial cells
Building regulatory networks often requires trade-offs between accuracy and speed. Here the authors show in a bistable network the transition from a slow decision making system to a rapid one dominated by small number fluctuations.
- Ferdinand Greiss
- , Shirley S. Daube
- & Roy Bar-Ziv
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Article
| Open AccessVortex phase matching as a strategy for schooling in robots and in fish
Whether and how fish might benefit from swimming in schools is an ongoing intriguing debate. Li et al. conduct experiments with biomimetic robots and also with real fish to reveal a new behavioural strategy by which followers can exploit the vortices shed by a near neighbour.
- Liang Li
- , Máté Nagy
- & Iain D. Couzin
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Article
| Open AccessLearning the non-equilibrium dynamics of Brownian movies
A tracking-free approach by Gnesotto et al. is developed to distinguish active and thermal fluctuations in microscopy data of non-equilibrium systems such as cell membranes. The method relies on a dimensional reduction scheme revealing a hierarchy of the most dissipative dynamical components.
- Federico S. Gnesotto
- , Grzegorz Gradziuk
- & Chase P. Broedersz
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Article
| Open AccessA particle-field approach bridges phase separation and collective motion in active matter
Interacting self-propelled particles exhibit phase separation or collective motion depending on particle shape. A unified theory connecting these paradigms represents a major challenge in active matter, which the authors address here by modeling active particles as continuum fields.
- Robert Großmann
- , Igor S. Aranson
- & Fernando Peruani
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Article
| Open AccessMechanical forces drive ordered patterning of hair cells in the mammalian inner ear
The periodic organization of cells is typically associated with mechanisms based on intercellular signaling such as lateral inhibition and Turing patterning. Here the authors show that hair cells in the inner ear rearrange gradually into a checkerboard-like pattern through a tissue-wide shear motion that coordinates intercalation and delamination events.
- Roie Cohen
- , Liat Amir-Zilberstein
- & David Sprinzak
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Article
| Open AccessLearning molecular dynamics with simple language model built upon long short-term memory neural network
Artificial neural networks have been successfully used for language recognition. Tsai et al. use the same techniques to link between language processing and prediction of molecular trajectories and show capability to predict complex thermodynamics and kinetics arising in chemical or biological physics.
- Sun-Ting Tsai
- , En-Jui Kuo
- & Pratyush Tiwary
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| Open AccessIn primary airway epithelial cells, the unjamming transition is distinct from the epithelial-to-mesenchymal transition
During repair, development, or cancer metastasis, epithelial cells can become migratory through partial or full epithelial to mesenchymal transition (EMT). Here, the authors report that differentiated epithelial collectives may undergo cooperative and collective migration without evidence of partial EMT through an unjamming transition (UJT).
- Jennifer A. Mitchel
- , Amit Das
- & Jin-Ah Park
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Article
| Open AccessHuman running performance from real-world big data
Laboratory performance tests provide the gold standard for running performance but do not reflect real running conditions. Here the authors use a large, real world dataset obtained from wearable exercise trackers to extract parameters that accurately predict race times and correlate with training.
- Thorsten Emig
- & Jussi Peltonen
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Article
| Open AccessHaloarchaea swim slowly for optimal chemotactic efficiency in low nutrient environments
Brownian motion places the ultimate limit on microorganisms’ ability to navigate. Thornton et al. show that Haloarchaea have a strategy of slow swimming and infrequent reorientation that exploits the randomising nature of Brownian motion to achieve optimal chemotaxis at the thermodynamic limit.
- Katie L. Thornton
- , Jaimi K. Butler
- & Laurence G. Wilson
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Article
| Open AccessGeometric pinning and antimixing in scaffolded lipid vesicles
Lipid bilayers feature an intricate interplay between membrane geometry and its chemical composition but lack of a model system with simultaneous control over membrane shape and composition prevented a fundamental understanding of curvature-induced effects. Here the authors demonstrate that the local substrate geometry and global chemical composition of the bilayer determine both the spatial arrangement and the sorting of lipid domains.
- Melissa Rinaldin
- , Piermarco Fonda
- & Daniela J. Kraft
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Article
| Open AccessSpatially selective manipulation of cells with single-beam acoustical tweezers
Acoustical tweezers can exert forces several orders of magnitude greater than optical tweezers but the absence of spatial selectivity and their limited resolution has prevented their use for many applications in microbiology. Here the authors perform spatially selective contactless manipulation and positioning of human cells.
- Michael Baudoin
- , Jean-Louis Thomas
- & Alexis Vlandas
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Article
| Open AccessTriacylglycerols sequester monotopic membrane proteins to lipid droplets
Triacylglycerols (TG) are synthesized at the endoplasmic reticulum (ER) bilayer and packaged into monolayer lipid droplets (LDs), but how proteins partition between ER and LDs is poorly understood. Here authors use synthetic model systems and find that proteins containing hydrophobic membrane association domains strongly prefer monolayers and that returning to the bilayer is unfavorable.
- Lucie Caillon
- , Vincent Nieto
- & Abdou Rachid Thiam
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Article
| Open AccessCollective cell mechanics of epithelial shells with organoid-like morphologies
The physical origins of man-made tissue morphologies with organ-like microscopic anatomy and functionality remain poorly understood. Here, authors propose a mechanistic theory of these structures, employing a 3D vertex model to reproduce the characteristic morphologies such as branched shapes.
- Jan Rozman
- , Matej Krajnc
- & Primož Ziherl
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Article
| Open AccessDirectional translocation resistance of Zika xrRNA
Zika xrRNAs survive in host cells because they can be unwound and copied by replicases, but resist degradation by exonucleases. Here authors use atomistic models and simulations and uncover that pulling into a pore the xrRNA \({3}^{\prime}\) end, as done by replicases, causes progressive unfolding; pulling the \({5}^{\prime}\) end, as done by exonucleases, triggers molecular tightening.
- Antonio Suma
- , Lucia Coronel
- & Cristian Micheletti
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Article
| Open AccessPolymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation
The molecular and physical mechanisms underlying chromatin folding at the single DNA molecule level remain poorly understood. Here, the authors use polymer modeling to investigate the conformations of two 2Mb-wide DNA loci in normal and cohesin depleted cells, and provide evidence that the architecture of the studied loci is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules.
- Mattia Conte
- , Luca Fiorillo
- & Mario Nicodemi
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Article
| Open AccessLarge-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models
Explicit molecular modelling of biological membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Here authors present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics which facilitates efficient simulation of large biomembrane systems.
- Mohsen Sadeghi
- & Frank Noé
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Article
| Open AccessAnisotropic ESCRT-III architecture governs helical membrane tube formation
ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here, the authors use cryo-ET, cryo-EM and mathematical modeling to reveal how the shape of the helical membrane tube arises from the assembly of two distinct bundles of helical filaments.
- Joachim Moser von Filseck
- , Luca Barberi
- & Aurélien Roux
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Article
| Open AccessMagnetic cilia carpets with programmable metachronal waves
Synthetic hair-like structures (cilia) controlled by an external field have been developed, especially for microfluidic applications. Here, Gu et al. make soft artificial cilia carpets with programmable magnetization patterns and utilize them to achieve pumping and locomotion in a soft robotic model.
- Hongri Gu
- , Quentin Boehler
- & Bradley J. Nelson
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Article
| Open AccessExtreme active matter at high densities
While active matter exhibits unusual dynamics at low density, high density behavior has not been explored. Mandal et al. show that extreme dense active matter, shows a rich spectrum of behaviour from intermittent plastic bursts and turbulence, to glassy states and jamming in the limit of infinite persistence time.
- Rituparno Mandal
- , Pranab Jyoti Bhuyan
- & Madan Rao
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Article
| Open AccessA transition to stable one-dimensional swimming enhances E. coli motility through narrow channels
Most biological and artificial self-propelled particles tend to be attracted by solid walls on their swimming pathways. Vizsnyiczai et al. show that, unexpectedly, confining E. coli cells inside a channel triggers stable locomotion along the channel axis once the channel is narrower than a critical value.
- Gaszton Vizsnyiczai
- , Giacomo Frangipane
- & Roberto Di Leonardo
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Article
| Open AccessHigh-throughput cell and spheroid mechanics in virtual fluidic channels
High-throughput rheological measurements of cells and cell clusters by microfluidics is limited by fixed channel dimensions. Here the authors create virtual fluidic channels inside the cuvette of commercial flow cytometers to dynamically tune channel cross section to enable rheological measurements from cells and cell clusters.
- Muzaffar H. Panhwar
- , Fabian Czerwinski
- & Oliver Otto
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Article
| Open AccessDense active matter model of motion patterns in confluent cell monolayers
Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes. Here the authors show that cell motility coupled to the collective elastic modes of the cell sheet is sufficient to produce characteristic swirl-like correlations.
- Silke Henkes
- , Kaja Kostanjevec
- & Eric Bertin
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Article
| Open AccessEnergy consumption and cooperation for optimal sensing
Cells exhibit exceptional chemical sensitivity, yet we haven’t fully understood how they achieve it. Here the authors consider the mutual information between signals and two coupled sensors as a proxy for sensing performance and show its optimisation depending on noise level and signal statistics.
- Vudtiwat Ngampruetikorn
- , David J. Schwab
- & Greg J. Stephens
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Article
| Open AccessControlled division of cell-sized vesicles by low densities of membrane-bound proteins
Membrane fission of a cell into two daughters is a core ability of cell-based life. Here the authors show that in artificial cells division can be controlled by regulating membrane curvature using low protein density.
- Jan Steinkühler
- , Roland L. Knorr
- & Reinhard Lipowsky
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Article
| Open AccessPhysical and behavioral adaptations to prevent overheating of the living wings of butterflies
Butterfly wings have low thermal capacity and thus are vulnerable to damage by overheating. Here, Tsai et al. take an interdisciplinary approach to reveal the organs, nanostructures and behaviors that enable butterflies to sense and regulate their wing temperature.
- Cheng-Chia Tsai
- , Richard A. Childers
- & Nanfang Yu
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Article
| Open AccessGeometric cues stabilise long-axis polarisation of PAR protein patterns in C. elegans
In the C. elegans zygote, (anterior) aPAR and (posterior) pPAR proteins are key to polarity maintenance, what factors determine the selection of the polarity axis remains unclear. Here authors formulate a reaction-diffusion model in realistic cell geometry and find that long-axis polarisation is promoted by cytosolic dephosphorylation at onset and its steady state determined by minimising the length of the aPAR-pPAR interface.
- Raphaela Geßele
- , Jacob Halatek
- & Erwin Frey
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Article
| Open AccessAnnexin-V stabilizes membrane defects by inducing lipid phase transition
Annexins are cytoplasmic proteins, which bind to membranes exposing negatively charged phospholipids in a Ca2+-dependent manner. Here the authors use high-speed atomic force microscopy and other techniques to show that annexin-V self-assembles into highly structured lattices that lead to a membrane phase transition on PS-rich membranes.
- Yi-Chih Lin
- , Christophe Chipot
- & Simon Scheuring